RUTLAND — Federal prosecutors said the mountain of evidence they presented during the last two weeks proves Frank Caraballo killed Melissa Barratt.

But defense attorneys in the case reduced the evidence down to a question of who the jurors believe — Caraballo or his former partner in drug sales, Joshua Makhanda-Lopez.

“It comes down to who you believe, Frank or Josh,” defense attorney Mark Kaplan told the jurors.

The defense and prosecution presented closing arguments Tuesday in the federal murder trial in U.S. District Court in Rutland. Jurors began deliberations Tuesday afternoon but were released after about two hours. They return today at 9 a.m. to continue deliberations.

Prosecutors say the two men were the only ones present when the Brattleboro woman was killed with a single gunshot to the back of the head July 28, 2011. The gun was never found and no forensic evidence exists that could directly connect someone to the crime.

Police did find at the scene a 9 mm shell casing which a forensic examiner told the jury could only have been fired from a Glock semiautomatic based on markings on the spent cartridge and bullet fragments.

Another witness in the case testified that he traded just such a gun to Caraballo days before the shooting. But whether proof exists to show that Caraballo was the shooter is up to the jury to decide.

During the trial, the jury heard from both Caraballo and Makhanda-Lopez as well as a variety of other witnesses who testified about Caraballo’s illegal drug operation and events they saw on the morning of July 28, when Caraballo confronted Barratt about $10,000 worth of drugs he suspected she had stolen.

Assistant U.S. Attorney Paul Van de Graaf said those accounts taken collectively gave weight to the government’s case that Caraballo killed Barratt in anger over his losses.

But perhaps the most powerful piece of evidence, according to the prosecutor, was a taped phone call that Caraballo made to his imprisoned half-brother minutes before he confronted Barratt.

“During that call alone, the defendant makes significant admissions about two issues — the scope of his drug business and his belief that Melissa Barratt stole drugs from him and that she was going to pay if he didn’t get them back,” Van de Graaf said.

“In that recording he is mad about his drugs,” the prosecutor added. “He told his brother he wanted to hurt somebody and he’s not going to take it as a loss.”

Makhanda-Lopez and Danielle Clemons, who was Barratt’s roommate at the time, later testified that Caraballo threatened Barratt and everyone else in the room with a handgun during a confrontation inside the women’s apartment.

Caraballo would later take the stand and testify that Makhanda-Lopez was the one who was armed in the apartment. And he said he didn’t threaten Barratt; he asked her for help selling drugs to pay back what he owed.

Van de Graaf said that account was unbelievable.

“The defendant’s story makes no sense,” he said. “Do you believe he used the word ‘please’ and asked that nicely?”

But Kaplan encouraged the jurors to ask themselves if Makhanda-Lopez was more believable than his client.

Makhanda-Lopez, he said, had every incentive to lie because of a deal he reached with the government that capped his potential prison sentence at 13 years on federal gun and drug convictions. That deal called for his cooperation and testimony in Caraballo’s trial.

“It’s an unbelievably favorable plea agreement for the crimes he committed,” Kaplan said. “Can you convict someone on his testimony? You can never tell if he’s telling the truth.”

Kaplan also asked jurors to consider an alternative narrative for Barratt’s killing.

In Caraballo’s version of the confrontation inside the apartment, Makhanda-Lopez pulled a handgun from his waistband at one point.

Kaplan asked the jury to consider the move as an implied threat to Barratt, who he theorized was working in cooperation with Makhanda-Lopez to steal the $10,000 worth of drugs from Caraballo.

“Why wouldn’t Melissa have raised her hand at some point during this conversation and say ‘I did it’?” he said. “I submit to you there is a reason why she didn’t. ... When she saw the firearm sitting on (Makhanda-Lopez’s) lap she got the message.”

Kaplan didn’t extend that scenario to Barratt’s killing in the woods of Dummerston, but he said it was possible that Makhanda-Lopez or another man — possibly Caraballo’s drug source in Massachusetts known only as “Dough Boy” — could have pulled the trigger.

Caraballo, he said, didn’t know who did it because he was on his way to Massachusetts with his girlfriend, Pamela Zygmont, who drove to Vermont to pick him up after the confrontation at the apartment.

But Van de Graaf said phone records debunked that theory.

While cellphone recordings indicate that Caraballo’s girlfriend did drive to Vermont on the afternoon of the July 28, phone records also show that she made multiple calls and sent multiple text messages that all went unanswered to Caraballo’s cellphone between 1:49 and 2:25 p.m. that day. Van de Graaf told jurors it was during that time that Barratt was executed.

“Isn’t the most likely scenario that she was driving up here because she was freaking out about what was happening that day?” the prosecutor asked, referring to phone calls between Caraballo and his Zygmont earlier that day.

Zygmont was never called as a witness by either side in the trial.

She reached a plea agreement with federal prosecutors on two counts of conspiracy to distribute narcotics, but the deal doesn’t require her to cooperate in prosecuting Caraballo.

She was named as a potential witness for the defense but was never called during the trial. Zygmont filed a motion challenging the defense’s subpoena on the grounds that she was invoking her Fifth-Amendment right against self-incrimination. A ruling on her motion was never issued.